After much testing and experimenting, I think I've got the search page working in eXist 2.1 (running under jetty). The newer version of eXist (and/or the lucene extensions) handle default or implicit namespaces differently.

Original code looked something like this:

for $match in $utter//exist:match
let $summary := kwic:get-summary($expanded, $match, <config xmlns="" width="40"/>)
for $line in $summary//self::p
return

The p element is introduced by the kwic:get-summary function, and the question is what namespace that element is deemed to be in. In the older version of eXist, the code above worked. In eXist 2.1, that code returned nothing. I don't know what namespace that p is in, so Martin suggested the wildcard namespace:

for $match in $utter//exist:match
let $summary := kwic:get-summary($expanded, $match, <config xmlns="" width="40"/>)
for $line in $summary//self::*:p
return

and that worked.

I had to work through similar issues with the span elements that kwic embeds within the p element. They too are in some limbo namespace so my code had to include the wildcard namespace selector. In addition, the span outputted to the page included an xmlns="" attribute, and that caused the css to fail to select it.
Original code (worked in eXist 1.4)

for $line in $summary//self::p
let $before := $line/span[@class='previous']
let $match := $line/span[@class='hi']
let $after := $line/span[@class='following']
return
<li>
<a href="player.xql?id={$id}&start={$startTime}" title="{$start}"> {$before} {$match} {$after} </a>
</li>

Modified code (works in eXist 2.1)

for $line in $summary//self::*:p
let $before := $line/*:span[@class='previous']
let $match := $line/*:span[@class='hi']/text()
let $after := $line/*:span[@class='following']
return
<li>
<a href="player.xql?id={$id}&start={$startTime}" title="{$start}"> {$before} <span class="hi">{$match}</span> {$after} </a>
</li>

As the span is coming from the lucence kwic extension, it will be only text, so I don't think explicitly grabbing only the text should cause me any problems, and it allows me to then code in the containing span, which renders properly on the page.